If you wish to align only two draft genomes, or align a draft genome against a complete genome, it is best to use the MCM algorithm, which is covered in Exercise 2. This option will not order contigs, and users should be aware that incorrectly ordered contigs will appear as genome rearrangements in the Mauve viewer. If one or more genomes are represented by a sequence list, and progressiveMauve is chosen as the algorithm, Geneious will concatenate the contigs from each genome into a single sequence for the alignment. It is also possible to align draft genomes, where each genome is represented by a list of contigs. Note: in this example we are using complete genomes where each genome is a single contiguous sequence. For a full description of the parameters, see here. All other settings should be kept at the default settings. Ensure the Mauve Genome tab is selected, and the algorithm is set to progressiveMauve. Then go to Align/Assemble → Align Whole Genomes. These are complete genomes downloaded from NCBI. In this exercise you will create an alignment of 3 Mycobacterium genomes.
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